# install.packages('tmap')
# install.packages('gdalUtils')
# install.packages('ggmap')
# library(ggmap)
library(raster)

## Warning: package 'raster' was built under R version 3.4.4

## Loading required package: sp

## Warning: package 'sp' was built under R version 3.4.4

library(sf)

## Warning: package 'sf' was built under R version 3.4.4

## Linking to GEOS 3.6.1, GDAL 2.2.3, proj.4 4.9.3

library(dplyr)

## Warning: package 'dplyr' was built under R version 3.4.4

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:raster':
## 
##     intersect, select, union

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

sosData <- read.csv("H:\\SOS_Project\\analysisData\\SOSdata_20180614_forARS.csv")


datumCount <- sosData %>%
  group_by(GPS_DATUM) %>%
  summarise(count = n())
  

sosWGS <- sosData %>%
  filter(GPS_DATUM=="WGS84") %>%
  na.omit()

## Warning: package 'bindrcpp' was built under R version 3.4.4

# 
# shortWGS <- slice(sosWGS, 1:5)
# shortWGS <- shortWGS %>% 
#   mutate(lon = as.numeric(as.character(shortWGS$LONGITUDE_DECIMAL)), 
#          lat = as.numeric(as.character(shortWGS$LATITUDE_DECIMAL)))

# 
# ###trying the process with ggplot
# corvallis <- c(lon = -123.2620, lat = 44.5646)
# 
# # Add a maptype argument to get a satellite map
# corvallis_map_sat <- get_map(corvallis, zoom = 3)
# 
# #point date set 
# coords <- cbind(as.numeric(shortWGS$LONGITUDE_DECIMAL), as.numeric(shortWGS$LATITUDE_DECIMAL))
# 
# 
# # Edit to display satellite map
# ggmap(corvallis_map_sat) +
#   geom_point(aes(lon, lat), data = shortWGS)

nrow(sosWGS)

## [1] 4846

names(sosWGS)

##  [1] "NAME"              "GENUS"             "SPECIES"          
##  [4] "FAMILY"            "ABBREV_NAME"       "COLL_DT"          
##  [7] "COLL_YR"           "ACC_NUM"           "COLL_NUM"         
## [10] "COLL_ID"           "SECONDARY_ID"      "PHYTOREGION_FULL" 
## [13] "SUB_CNT1"          "SUB_CNT2"          "SUB_CNT3"         
## [16] "GEOG_AREA"         "LOCALITY"          "LATITUDE"         
## [19] "LONGITUDE"         "LATITUDE_DECIMAL"  "LONGITUDE_DECIMAL"
## [22] "GEOREF_SOURCE"     "GPS_DATUM"         "ALTITUDE"         
## [25] "ALTITUDE_UNIT"     "LAND_OWNER"        "KEYWORD"          
## [28] "MISC"

latLonWGS <- sosWGS %>% 
  mutate(lon = as.numeric(as.character(sosWGS$LONGITUDE_DECIMAL)), 
         lat = as.numeric(as.character(sosWGS$LATITUDE_DECIMAL))) %>%
  filter(!is.na(lon)) %>%
  filter(!is.na(lat))

## Warning in evalq(as.numeric(as.character(sosWGS$LONGITUDE_DECIMAL)),
## <environment>): NAs introduced by coercion

## Warning in evalq(as.numeric(as.character(sosWGS$LATITUDE_DECIMAL)),
## <environment>): NAs introduced by coercion

coords <- cbind(latLonWGS$lon, latLonWGS$lat)
nrow(coords)

## [1] 4832

points <- SpatialPointsDataFrame(data = latLonWGS,
                        coords = cbind(latLonWGS$lon, latLonWGS$lat),
                        proj4string = CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs"))

library(gdalUtils)

## Warning: package 'gdalUtils' was built under R version 3.4.4

library(tmap)

## Warning: package 'tmap' was built under R version 3.4.4

tmap_mode("view")

## tmap mode set to interactive viewing

qtm(shp=points)

tm_shape(shp=points)+
  tm_dots()